Hope and Love will Triumph
by Short Angel
Summary: While trying to recover from the events of TMC John and the rest of Atlantis team discover that something is out in Pegasus waiting for them to find it. Chapter 11 up. J/E. R/T, J/S *possible spoilers for S4!
1. Mourning

Title: Hope Will Triumph

WARNING: Spoilers for S4, this will be an AU of S4,

Disclaimer: None of the Stargate Atlantis characters are mine, as much as I may wish.

Summary: Starts right after This Mortal Coil. Knowing that Elizabeth Weir is gone after the events of This Mortal Coil, John Sheppard and the rest of Atlantis team try and move on. But they still can't shake the feeling that somewhere out in Pegasus there's something, or someone worth looking for. Horrible summary yes I know.

A/N: This is my first Stargate Atlantis fic, so please bare with me while I get this show on the road. Enjoy.

_Atlantis_

John Sheppard sat heavily on his bed, running his hands over his face, still in his dress blues. It felt like he had aged ten years today. Looking through his hands his eyes wandered over the room, despite the changes in Atlantis over the last few months and the neglect it had faced; somehow it had stayed as though nothing had happened.

_'Ironic isn't it? We have a year out of hell and this city goes on just like nothing happened'. _The bitter thought passed through John's mind before he could stop it. His eyes fell on part of the reason for the pain he and other Atlantis personnel were feeling at the moment. On the bed next to him sat the pot he gave Elizabeth Weir for her birthday during their first year of Atlantis. Next to that was her father's pocket watch; he had told Rodney that he was sending all her things back to Earth, but after further review he couldn't send these two items, one signified their first year in Atlantis, the other the nights he found her toying with the watch.

Tears gathered in the corners of John's eyes as he picked up the watch. How many times did he see her playing with the thing after a difficult decision, or after his team had just got back from a disastrous offworld mission? Atlantis wasn't going to be the same without Elizabeth Weir, her way of command, giving people like him chances, the late night balcony talks, these were some of the things that made Atlantis, Atlantis. Nothing could ever fill the void left there, not another leader, though Sam Carter had done her best, there was only one leader for Atlantis and she was gone.

John got up and looked out at the city he had come to call home. Rain poured down in sheets, as if the planet itself was mourning along with them. The ceremony earlier was simple and short, there was no body to view or send back to Earth. A quiet gathering, Rodney had given the eulogy, and was surprisingly elegant. Teyla stood next to Ronan, tears silently coming down her face while Ronan had stood silent, fighting to contain his emotions. Later at the reception, Teyla had come up to John and told him that her baby's middle name would be Elizabeth in honor of the fallen leader. Just after he saw Sam Carter and Jack O'Neill talking quietly in the corner, he knew Elizabeth had been in charge of the SGC briefly, but hadn't expected the general to come to the Pegasus Galaxy to say good-bye. He was touched, touched truly, and he was sure if Elizabeth could see she would have been too.

As John watched the rain fall he saw the lights of Atlantis shut down slowly, and some cries of shock as the lights went out on people that were still up.

"What's going on?" John asked into his earpiece, unconsciously gripping the watch tighter.

"Yes Rodney, what's going on?" Sam's voice came over the earpiece.

"I don't know, hang on a second!" The astrophysicist yelled.

"Rodney…" John was getting aggravated.

"It seems…" Rodney's voice broke. "That Atlantis is mourning."

"What?" Sam was confused.

"Look at a laptop that's connected to the city's mainframe. They're battery powered so they still should work." Rodney said quiet.

John raced over to his laptop and powered it on. As soon as the screen loaded completely Atlantis' message was shown in clear script across the screen. "LONG LIVE ELIZABETH WEIR, THE FIRST LEADER OF ATLANTIS!!!! MAY SHE FINALLY FIND PEACE."

"Truer words have never been spoken," John murmured, looking at the pocket watch. He looked out at the city. "Even Atlantis misses you Elizabeth. Rest easy." The words came easy and hard now that she was gone. "I love you."

_Elsewhere in Pegasus:_

Deep green eyes gazed out at the sea of stars as the ship silently traveled through space. The eyes narrowed in hate as they saw a Replicator vessel attacking a Wraith ship, her second in command was awaiting her order. Turning she spoke harshly, "Destroy them."

"Yes ma'm."

The woman went back to looking at the stars from a different window, not wishing to see the battle. Sadness filled her as she looked at the planet that Atlantis once called home. _'John'._ She hoped he was staying out of this war.


	2. Advice and Discoveries

Chapter 2- Advice and Discoveries

A/N: Thanks for all the kind reviews! On with the show!

_Atlantis: two weeks later_

Sam Carter, new leader of Atlantis, stood at her office windows, feeling like an alien in the city she had come to call home. People in this city were tight-knit and, though welcoming towards her, still mourning their former leader. Watching the bustle of the Gateroom, she felt isolated, people greeting one another cheerfully, as though they have known one another their entire lives. Looking around, Sam hoped that one day she would be allowed to join in too, but she knew that time would come after the decorations of black that covered the Gateroom walls in honor of Elizabeth came down. Glancing at her watch, Sam turned back towards her office: there was only fifteen minutes until Colonel Sheppard's team returned from off world.

In the meantime, Sam had something that would occupy her time. Jack had e-mailed and she really needed to reply back, and now that Atlantis had almost fully come back online, she was able to. The process had begun the day after the ceremony; apparently Atlantis had felt that more time was needed before normal operations were to continue, and had set a slow but steady pace to allow her systems to come back online. Opening the e-mail, Sam smiled at what her former commanding officer had to say.

_Carter,_

_How are things going? Is Atlantis still shutting itself off to you guys? I have suffered through so many meetings I haven't had time to even think, let alone talk. I think a fishing trip is in order. Maybe I'll drag Teal'C and Daniel along, they need a break too. _

_Though, on the subject of meetings, I met with Elizabeth's mother the other day. I hate those types of __meetings;__ nothing you say seems to be enough. "She served her country well and died bravely" doesn't seem to cut it. Either way, she was still happy I took the time to visit and return Elizabeth's things to her. _

_You were worried that your letter was too impersonal, well don't, she loved it. It's never easy to write letter like that, you can't tell the person how __really__ or where their loved ones died. Take it from a pro, it never gets any easier. Though nice touch letting the senior staff of Atlantis write letters too. Mrs. Weir told me to thank you all __personally__ and that it is so nice that to know her daughter had such good friends __and people__ who cared about her. BTW- who knew McKay could write with feeling?_

_Let me know how things are going for you. Tell Sheppard no suicide missions, or I imagine Elizabeth will come back and kick his ass._

_Jack_

_P.S. Do you know anything about a pocket watch? It was Elizabeth's dads and he gave it to her. It should have been in the box of her stuff, but wasn't. Though Mrs. Weir said that if someone there wanted to keep it go ahead, it's a small comfort. All she wants is to know the person who has it._

Sam smiled, knowing how hard it was for Jack to put his meeting with Elizabeth's mom in words. At least she now knew that her letter had offered some comfort. Quickly Sam sent the e-mail out to the other members of the senior staff; they deserved to know how the meeting went as much as she did. Settling back, Sam began her reply.

_Sir,_

_Things are going as well as can be expected here. Atlantis has been slowly allowing us back in, just this morning we got e-mail back. Fishing sounds like it would be perfect to relax you, but in a way I feel sorry for Teal'C and Daniel. Still though, I kind of wish I won't miss it._

_I'm glad Mrs. Weir got some comfort out of my letter. I was worried that mine sounded too impersonal. I'll make sure that the other senior staff knows how Mrs. Weir received their letters. I imagine Rodney only writes with emotion when he wants to. Somehow Elizabeth managed to gain his respect I imagine, no small feat I know._

_Tell Daniel and Teal'C hi for me, and that I miss them. Hopefully things will start becoming normal around here, or as normal as things get here in Pegasus. As for the pocket watch, I wasn't even aware there was one. As far as I know everything of Elizabeth's was in the box._

_ Sorry I can't be of more help. _

_Sam_

As Sam clicked send, the Stargate sprang to life. "Offworld Activation!" Chucked called. Sam rushed out into the Control Room, duty called.


	3. Battle Plans

Chapter 3

A/N: I must say there is a lot of irony in this chapter, I wrote it prior to the airing of BAMSR and that end scene with Elizabeth was too close to this for comfort. Still I like my AU better, hopefully this will clear up some questions from previous chapters. And so my lovely readers we are temporarily leaving Atlantis and venturing back to the far reaches of Pegasus. Enjoy

_Somewhere in Pegasus:_

Elizabeth Weir was a changed woman, commander of an Asuran vessel, with a mission to wipe out both Wraith and Asurans alike. Wiping out the Wraith couldn't be helped, the command was included now in the base code of her nanites; but unlike other Asurans her humanity kept the urge in check. Maybe once both races were destroyed, she could finally find peace, never back in Atlantis where she wanted to be, but on some quiet planet, where she could still do the things she had wanted to do when the Atlantis expedition originally arrived in Pegasus.

She still wondered how she had managed to convince Oberath that her humanity had died and she could be trusted, but didn't want to question her luck. After she convinced Oberath she then rose in the in the Asuran ranks. Oberath had given her command of this ship with the orders to destroy the Wraith. Over time, Elizabeth realized that she could subtly change the code in those she commanded, so much that, while she could never remove the Wraith code, she could also add a code to help destroy Asuran vessels as well, and leave the humans alone. A constant process that took a lot of subconscious concentration on her part, in worry that the Asurans aboard the ship would find a way to override her commands.

This kept Atlantis safe while eliminating threats on the other side. To Oberath, she was the perfect human made machine. To her crew, she was the perfect leader. And to Elizabeth, she was a tool turned against those who had tried to make her that way. Her body may have healed, but she could still feel and remember every amount of torture both physically and mentally afflicted upon her before she could manipulate Oberath, making her hate the Asurans enough to pursue them as she did.

Walking to the bridge, her second in command awaited her. "What is going on?" Elizabeth asked, folding her arms across her chest.

"Lord Oberath is on the move, ma'am. Rumor has it that he is mounting a last chance offensive here." He pointed at a planet on the holographic map.

Elizabeth studied the map; the planet was right next to New Athos which she knew had the new address for Atlantis; it was too close for her comfort. "How long until they get there?"

"A few weeks at the most."

"How much time until we can get there ourselves?"

"The battle will have all ready been fought, and a winner decided."

Elizabeth looked thoughtful, that wouldn't do at all. "Where is the nearest Wraith vessel to our location?"

"Two hyperspace jumps ma'am." Another technician spoke up.

"Send a message to the Wraith saying that intelligence says the Asurans are attempting to mount a major offensive in the area, and that they should request immediate reinforcements. Disguise the transmission as if it was coming from another Wraith vessel. Also tell them that we will be joining them as well. Send a message to the Asurans telling them that the Wraith are doing the same. We let them wipe each other out or at least attempt to, and clean up what survives, so far all of our offensives have been successful, it is time to go on a bit larger scale."

"Yes, ma'am. Right away," the second-in-command hurried off to follow through with the order. Elizabeth watched him hurry off, smiling, Oberath may have thought he had done something by completely making her "Asuran", but he was about to find out how drastically wrong he was.

_Replicator Ship, Elizabeth's Quarters_

Elizabeth ran her fingers through her hair, trying to unwind before the battle ahead. So far things were going according to plan; both the Asurans and Wraith had fallen for the messages almost too easily. She just felt lucky that none of her people could connect to the collective to alert Oberath about their leader's deception towards him.

_'It's funny, I have always worked against deception, and military force, and here I am doing exactly what I have hated all my life.' _Elizabeth sighed. _'Then again personal morals and Pegasus don't always mix.' _ She recalled the decision to use the retrovirus against the Wraith, and how much that had kept her up at night.

_'__Ahh__…Atlantis, how I miss you." _Elizabeth smiled as her memories of Atlantis flowed through her mind. These were the memories that kept her sane through the torture, and had helped keep her in touch with her humanity. Calling up her favorite memories of Atlantis, Elizabeth settled down to sleep. John giving her the Athosian jar, she never found out how he knew it was her birthday. _'That will be something I'll have to ask when I see him again.'_ Smiling she closed her eyes and fell asleep. _'Good-night John. Everyone.'_


	4. Briefing

Chapter 4- Briefing

A/N- Thanks for all the lovely reviews and alerts.

_Atlantis_

John was the first of his team into the Gateroom to be greeted by the familiar sight of guards and technicians standing by. Looking up at the overhang of the main control area his spirit fell suddenly as he saw Colonel Carter waiting to greet the arriving team. John sighed; yup this was going to take a lot of getting used to. He watched as Sam moved down the stairs to greet the team just as the wormhole disengaged.

"Colonel," John greeted.

"Colonel," Sam replied. "How was the mission?"

"Pretty straight forward. We came, we saw, we conquered. Well, without the conquering part."

"To say the least," Rodney spoke up. "Sam you won't believe what we saw on the planet..."

"However it can wait until the briefing." Teyla said, interrupting Rodney.

"All right then, briefing in one hour?" Sam asked and John nodded. Rodney looked furious. "You can tell me then, besides you need to visit the infirmary, and get changed. You'll appreciate the extra time."

"Come on, let's go." John led the way out of the Gateroom.

Out in the corridor, Rodney exploded. "What on Earth did you do that for? This could be the big break we were looking for!!"

"McKay, we don't even know if that damage was caused the way we think it may have been." John snapped back.

"That doesn't mean that she shouldn't know like immediately!"

"We still don't know, and so we tell her about it at the briefing," John said through clenched teeth. "We don't need to cause alarm without having all of our facts straight."

"But…"Rodney stammered.

"Shut-it McKay, you heard the man," Ronan grumbled. "Come on, let's go." He dragged a protesting Rodney down the corridor and towards the infirmary.

Teyla looked at John, concerned then noticed the fact he was holding something in his hand. She smiled softly at the sight of the pocket watch. "Do not blame him John; we have all been under a lot of stress lately."

"He's only acting like this because he has a crush on Carter," John grumbled. "Though I can't help but wonder if we should have told Carter."

"Well as you said, we have no proof right now, you were right to wait until our later briefing. I'm sure even deep down Rodney knows it as well." Teyla said. "Now come on, we don't want to keep the doctor waiting." Gently guiding, Teyla led John towards the Infirmary.

Teyla and Ronan walked through the corridors toward the Control Room trying to arrive on time for the briefing after an annoying half-an-hour in the infirmary.

"Can you believe McKay?" Ronan asked, trying to navigate the crowd.

"I'll tell you the same thing I told John, we can't blame him we have all been stress lately." Teyla said. "It's brought out some of the more unpleasant qualities in all of us."

"Well McKay's always been like that," Ronan muttered, then fell silent. "It's odd."

"What is?"

"Going to this briefing and knowing she won't be leading it," Ronan almost choked on his words. "It's even odder to think that we'll never see her again."

Teyla nodded sadly. "I know. But if the Ancestors are kind then Elizabeth's finally at peace."

"I hope so," Ronan said softly. "Well we know how McKay's taking it, but how do you think Sheppard's dealing with it?"

"As well as can be expected of him, I imagine. He was especially close to Elizabeth," Teyla said, looking up near the briefing room as they entered the Gateroom to see John talking to Sam. "I believe that he has found something of comfort, though."

"You mean the watch?"

Teyla's eyes widened. "You know?"

Ronan shrugged, as they climbed the stairs. "I see him playing with it a lot."

Both Sam and John looked up as they joined them. "Teyla, Ronan," Sam greeted as they joined them.

"Colonel," Teyla replied while Ronan just nodded in greeting. Teyla looked around. "Where is Rodney?"

"I don't know, but if he doesn't hurry we'll have to start without him," John said.

Suddenly footsteps could be heard running up the stairs, everyone's heads turned to see Rodney running towards them carrying a bunch of photos. "I'm here, don't start without me!!!"

"What's with that McKay?" John asked, gesturing towards the photos.

"For the briefing of course," Rodney shot back, looking like he couldn't believe that John was questioning him about it.

"Well since we're all finally here, let's get started," Sam said leading the way into the Briefing Room.

After everyone got settled in their seats and looked at John. "So how was the mission?"

John cleared his throat, "The planet itself was uninhabited and if there was a civilization at some point, it's been long gone."

Rodney coughed pointedly at this point. Sam turned towards him. "Yes Rodney?"

"If I may," he looked at John, who nodded. "We did find something on the planet though."

"What's that?" Sam asked.

Rodney stood and walked over to Sam to show her the photos he carried with him to the briefing. "On the planet there was wreckage of a wraith and replicator ship. It looked like they were fighting each other."

"What's new with that? Ever since you implanted the code in their nanites, the replicators have been after the wraith ever since," Sam pointed out.

"True, but if you see on the photos it looks like the hulls were damaged by something other than each other. Look at the direction of the shots, you can see other shots coming from a different direction, and that's what took them down."

"Another wraith ship, then?" Sam asked.

"That's what we thought, but it isn't," Ronan said.

"Yeah those shots came from another replicator ship," John added, while Rodney glared.

"So we have a renegade replicator ship out there somewhere?" Sam asked.

"It appears so, but also keep in mind this is the only piece of wreckage like this that any team has come across. So there is no way to be certain," Teyla said. "I can contact some of my people's allies and ask them to keep an eye out for similar wreckage."

"Go ahead," Sam said. "At the same time I want the city cloaked, we don't need them to find us right now." They nodded. "All right, dismissed."

Sam stayed behind and watched them all leave, John trailing behind the others. She watched as he pulled something out of his pocket, seeing the chain dangle from his hands she knew it was the missing pocket watch Jack had mentioned. Smiling sadly she knew she'd have to chat with John about it, he needed to know that she knew. That and she had to tell Jack to tell Mrs. Weir, and then again she may tell him to hold off and make an offer to John to do it. Sam sighed, maybe talking with Mrs. Weir would do him some good, at least she hoped.


	5. Talks

Chapter 5- Talks

A/N- And so my pretties it's time for John's moment of truth. This chapter/ fic may seem sort of Sam centric just because while I was coming up with the original idea, I was thinking about how awkward she must be feeling dealing with a city of people who are mourning the loss of someone close to them and still trying to fit in. For those who are still waiting for Sparky, don't fret we'll have Sparky a plenty in a little bit. Enjoy.

Sam had no way of predicting the chain of problems that would unfold on Atlantis in the following days. It had all started with Rodney attempting to power a bunch of super computers in his lab to detect the wraith. From what Sam got he was trying not only power the computers to monitor through Atlantis' systems, the entire Pegasus galaxy in order to locate the rouge replicator ship, but link them together and make them each show a different sector. The result was that the computers overloaded the section of Atlantis Rodney's lab was located in, which cause a blackout in that part of the city and exploding electronics where the overload went through. The most damage was in Rodney's lab itself, where all the computers he was using blew, almost killing him and causing severe damage. After that incident, it was if permission was given for all hell to break loose with more and more problems arising everyday since.

Today was the first day that no problems had happened, and Sam was taking full advantage of the break. After she got a bite to eat in the mess hall, she would be on her way to see John. Grabbing a tray, and moving through the line she looked around for a place to sit; seeing Teyla sitting alone, Sam opted to sit with her.

"M ay I join you?" Sam asked.

Teyla looked up from her lunch, "Of course." She smiled as the new leader of Atlantis sat down. "How has your day been?"

"Pretty uneventful really. McKay hasn't tried to blow up his lab, nor have any other problems occurred. It's a relaxing change."

"Ah, yes. He was complaining earlier that not only did he destroy his own work and now has to start from scratch, but he also had to repair the other damages from what he did and that it was hindering the work he was trying to restart. It kind of reminds me of the time he blew up a solar system."

Sam nearly spit out her drink, " What?! Leave it to McKay to do something like that. What happened exactly?"

"He was trying to find a way to defeat the wraith, and in the process blew up an entire solar system. Elizabeth and John were so upset with him. I don't think I ever saw Elizabeth that upset, not to mention John since he was the one who talked Elizabeth into going ahead with it." Teyla smiled sadly.

Sam nodded, "You were all close to her weren't you."

"You cannot help but be close here, but yes we were," Teyla paused. "Especially John.

"I can see why he kept the watch."

"You know about that too?"

"Well I didn't know it was missing until Jack, General O'Neill, told me about it. And then I saw him holding it after the briefing the other day. I was on my way to talk to him about it, and don't worry I won't make him give it back. In fact Mrs. Weir requested that once we found out who had it, that we let them keep it. She just wanted to know who has it."

Teyla breathed a visible sigh of relief, "That is good. It seems to be the only thing that has brought some comfort to him."

Sam nodded, "The question is do you know where he is right now. I need to talk to him about it, and let him know that I know."

"I believe that he is in his office doing some mission reports," Teyla replied standing.

Sam stood too, "Thank you Teyla." She started to leave.

Teyla nodded, "Don't worry Colonel, it will get easier for us all."

Sam nodded and then walked away.

Knocking on the door to John's office, Sam paced in front of it nervously. She had no idea how to go about this, not to mention how John would react when he found out she knew, and so in turn would Jack and Mrs. Weir.

"Come in," John called. It was now or never.

Sam slowly opened the door and took a look at the office for the first time since she had been given command of Atlantis. Reports piled in some places as tall as the ceiling, and the desk was covered with them. "Where are you?"

John's head poked up from behind a pile on his desk. "Oh there you are." Sam moved some reports from the chair in front of the desk and sat down.

"What can I do for you Colonel?" John asked.

"Well first off you can drop the formalities. I'm not here on official Atlantis business John."

John moved his chair beside the desk so they could actually see each other. "All right, but if you're not here for Atlantis business, then why are you here, it's a long way to come down here just to say hi."

"True," Sam agreed. "Actually I came to ask you about a pocket watch, it was Dr. Weir's dads. General O'Neill e-mailed me about it after he visited Mrs. Weir. I guess she brought it to Atlantis, but it wasn't among her things when they were returned to Earth." She watch John's eyes widen at the mention of the watch, and slightly fidget like a kid caught with his hand in a cookie jar.

"I haven't seen it, everything of hers that was on Atlantis was sent back to Earth, so it should have been in the box."

"That's what I thought too. It was actually Mrs. Weir who noticed it missing. She was wondering if anyone here could have kept it as a small comfort," Sam said, noticing John was once again figetting in his chair, looking very guilty.

John looked a guilty as he felt, still feeling that he owed the woman whose daughter he couldn't save, and had effectively abandoned on the Replicator home world. He figetted some more, tearing himself apart for keeping the watch in first place, by all rights it was still Elizabeth's and should have gone back to Earth for her mom.

Sam watched him feeling equally as guilty. _'Way to go Carter, you came here to talk to him and eventually have him tell you himself, not guilt him into it.' _

Enough was enough. "Listen John, I know you have it."

John's eyes widened to the size of small saucers. "Then there's no point in hiding it." He pulled the watch from his pocket and held it out in his open hand for Sam to take.

Sam shook her head, "I didn't come here to take it back John. Mrs. Weir only wanted to know who had it, that's all. She said whoever did was free to keep it if they so choose." Sam gently closed John's hand around the watch and pushed it back towards him.

"Really?"

Sam nodded, "That's what she said, for whatever comfort it's worth I believe. It's never easy to loose someone close to you and she realized how close all of you are out here. Even if she didn't know where exactly you all were." Sam paused. "Though I do have to ask, why are you here buried in mission reports?"

John shrugged, putting the watch back in his pocket. "Just trying to keep busy I guess."

"I see, just don't shut yourself off from everyone John, that's all I ask. They're all dealing with the same thing, and I know that Elizabeth wouldn't want it." Sam stood to leave.

"How did you find out?"

"I've been in Atlantis long enough to know that it's very, very hard to keep a secret here," Sam smiled. Well that, and I saw you playing with it after the briefing the other day."

"Oh," John said. "Sam…thanks. And tell Mrs. Weir thanks too."

"No problem, though I think you may want to tell her yourself. She may feel better hearing it from you than from Jack or I."

John looked thoughtful for a moment. "I'll do that." For the first time in a long time, John actually smiled.

"Good to hear," Sam replied and left smiling. Things were going to maybe turn out all right after all.


	6. Email Interlude

Chapter 6- E-mail Interlude.

A/N: Thanks for all the lovely reviews/ alerts!! Let's see what's up the Atlantis e-mail scene shall we? Expect a few of these, so if anyone was left out they will be included in the others, never fret. Enjoy.

_Dear Mrs. Weir,_

_I must admit I feel a bit odd writing you once again in such a short while, but at least these circumstances are a bit more joyful. I'm not sure, but by now General O'Neill would have told you what I have to. I was asked about Elizabeth's father's pocket watch a few days ago and was told that you found it to be missing among Elizabeth's belongings. To my shame I must admit that I have that watch. I kept it out of a way of small comfort, as well as a reminder of her and what I failed to do: Protect your daughter, and as such I feel responsible for what happened to her. _

_I guess my only comfort to you is that she died doing what she loved, being on the adventure of a lifetime, meeting new cultures and celebrating what brought us together as well as the differences. You may ask why I said nothing about the watch before, well, I guess I was afraid, afraid that someone would try and take that little comfort from me. _

_I am truly sorry for your loss,_

_LT. Colonel Jonathan Sheppard_

_Sir, _

_Well the pocket-watch mystery if finally solved, just do me a favor and say nothing to Mrs. Weir yet. I think John wants to tell her himself, and it will do him a world of good. Though seriously Sir, I never want to go through this again in my military career, or at this point, lifetime. _

_Though slowly now, things are starting to get slowly back to normal. Atlantis' systems have finally come back to full power, and Rodney has all ready succeeded in nearly blowing up a pier of the city where his lab is in an attempt to see replicator ships that are moving in every part of the galaxy. Don't ask. (See mission reports when we dial in next to see what lead to this.) So as of this point I really need to relax._

_Speaking of relaxing, how as your fishing trip? Did you actually get Daniel and Teal'c to go along? Let me know how things are Earth-side._

_Much love,_

_Carter_

_SAM!!!_

_SO I THINK I FINALLY HAVE THE HAND OF THIS E-MAIL THING, DANIEL'S BEEN SHOWING ME. SPEAKING OF WHOM, I THINK HE'S ANNOYED WITH ME. I GUESS IT ALL STARTED WITH ME TAKING A TEENSY, WEENSY, ARTIFACT FROM MG6778, THEY WON'T MISS IT BUT DANIEL AND CAM WOULDN'T HEAR IT. I NEED ANOTHER GIRL TO BACK ME UP HERE, THOUGH SPEAKING OF TREASURE IS THERE ANYTHING GOOD IN ATLANTIS? COME ON WITH ALL THOSE ANCIENT ARTIFACTS THERE HAS TOBE SOMETHING THAT PEOPLE WON'T MISS. _

_GENERAL O'NEILL WAS HERE THE OTHER DAY, GATHERING UP TEAL'C AND DANIEL FOR A FISHING TRIP, AND DANIEL WAS A TID BIT ANNOYED, THAT I WELL, KISSED HIM._

_ANYWAY, YOU NEED TO COME TO EARTH SOON SO WE CAN HAVE A GIRLS' NIGHT OUT!!!!_

_VALA_

_Sam,_

_VALA IS DRIVING ME INSANE!!! Not only did she steal that artifact, (which we didn't find out about until we got back to the SGC) but then she kissed me in front of Jack. He made a joke about bringing my wife and then she jumped in my arms and kissed me!!! I went with him to get away from her, and Teal'c came along just because. Though the entire trip he razed me for it. _

_So how are things in Atlantis, I still can't believe you got to make it there for premanent assignment before me. I can only imagine what you guys are finding out about. I'm still half tempted to jump on the Daedalus and hitch a ride over there._

_Daniel_

Subject: HELP!!

_Sam,_

_Help me out here because Jackson and Vala are driving me nuts!!! Ever since the artifact incident, they've been at each other's throats all the time. I seriously think Jackson's about to murder her._

_Any advice you can lend to the situation would be helpful._

_Cam_

Atlantis Memo

Subject: What the Hell??!!

_McKay,_

_So I am only going to ask this once, what the hell did you do to piss Carter off so much, and will you lay off? You've all ready blown up one pier while she's been here, don't go for it again. She looked like she was ready to blow when I saw her in the corridor earlier, muttering something about you. _

_Just so you know this isn't the way to whoo the woman._

_Sheppard._

RE: What the Hell??!!

_Sheppard,_

_Just for your information I did nothing to "piss her off" as you so delicately put it. I simply told her that my plan to moniter the galaxy for our dear rouge ship was coming along swimmingly. I've just finished connecting my computers with the deep space sensors here on Atlantis, and she's just mad because I'm smarter than her and figured out how to do it. And before you ask: No it won't over load the circuits, I've checked. And no I wouldn't have thought of this is in the first place, genius takes time. _

_Rodney_

_P.S- AND NO I AM NOT TRYING TO WHOO HER!!!! GOD, SHE'S BLONDE AND FAR LESS SMARTER THAN ME. WHAT IN THE WORLD ARE YOU THINKING. NOT EVERYONE IS KIRK HERE LIKE SOME PEOPLE WE KNOW!!!!_

It was late night in Atlantis and Rodney was where he was most days and nights now, staring at his computer screens trying to locate some trace of the replicator ship. So far he had been at his vigil for almost three days straight, only sleeping and eating when his teammates and Sam came and forced him to, and he was frustrated by the lack of results.

"Come on you stupid machines, come on!!! It can't hide forever!!! You should have found something by now," sighing, Rodney took a sip of his coffee.

Suddenly his personal laptop beeped in alert, and he rushed over to it, grinning. "Finally something!!! What do ya got for me?" Rodney took one look at the screen and his mouth dropped open and his eyes widened. Clicking his earpiece he spoke hurriedly. "Sheppard, Sam, Teyla and Ronan, meet me in the Control Room immediately. I found something you'll want to see." Breaking the connection before anyone could ask any questions, Rodney disconnected the laptop from it's power cord and took off for the Control Room.

A/N: Cliffhanger. I'm evil, yes I know. evil grin Well you know what to do. Chapter seven hopefully coming soon.


	7. Bad Day

Chapter 7- Bad Day

A/N and extended Disclaimer- As all ready stated I do not own the Atlantis characters, but I did create Juno and the rest of the replicators aboard Elizabeth's ship. This is just so people do not sue me, claiming I took their characters, I'm poor people!

Now that that necessary thing is said, thank you as always for the reviews and alerts, and Enjoy!

"Okay Rodney, we're all here. Now what did you want?" Sam asked once they had all assembled in the control center.

"Especially at this hour," John muttered, rubbing his eyes. "Some of us were trying to sleep."

Rodney choose to ignore him, too excited to pay much attention, as he was busying himself with connecting his laptop running the program to the large screen in the control room. "This." He finished his connection and a large map of a section of the Pegasus galaxy began to appear on screen. "I found this when my program to try and find the rouge ship that took out the ships on the planet we were just on."

"I thought we agreed that, it may not have been a rouge ship, and the marks on the hulls could have been from them firing on each other," Teyla said, watching the screen.

"Just in case then, eh?" The others just looked at him. "Look I was just trying to see if I could find a ship that was alone, and not really near any wraith ships." The image finally finished loading, and in the center was a bunch of blips that represented several wraith and replicator ships alike. "Only this is what I found."

"Are those what I think they are?" John asked.

"If you mean Replicator and Wraith ships, then yes." Rodney said, smirking proudly.

"What are they all doing there?" Sam asked, staring at the screen in a state of shock.

"I'd say they're getting ready for war," Ronon said.

"Thank you Captain Obvious," Rodney snarked. "But what is most interesting is over here." He widened the screen, and zoomed in on a solo ship. "I'll lay odds that, that is our rouge ship."

"Why does it appear that no ships are firing?" Teyla asked. "They only appear to be sitting there, if there is fighting shouldn't we see ships disappearing?"

"My guess is that the solo ship is cloaked," John began.

"But, they'll still show up on our sensors despite their cloak," Rodney interrupted.

"They're probably waiting for the order to fire," Ronon added to John's earlier statement.

"But what's the reason for the ship that's alone?" Sam wondered aloud.

"Well if they are connected with the wreckage on the planet, my guess is that it's waiting for the others to blow each other up, and clean up the survivors while they're damaged," John said thoughtfully.

"What now?" Ronon asked.

"We wait," Teyla said softly. "There is nothing we can do right now, but watch and wait."

_Battle Front, Elizabeth's Ship_

"We're holding position, cloaked as ordered ma'am," Elizabeth's second in command reported, or Juno as she named him, as she swept into the Bridge clad in her black leather outfit, that to some degree reminded her of her uniforms on Atlantis, only her coat had a longer tail in the back.

"Good , we don't want them to notice us until it's too late," Elizabeth smiled grimly, taking her seat in the captain's chair. "Everyone to their stations!"

"Lord Oberath's flagship has just entered the outer part of the solar system," Her navigation officer, Navi, reported.

Elizabeth looked out at the assembled fleet on both sides, "They won't attack until he has the chance to join the fun." She smiled. "Have weapons, and our sheilds ready at a moments notice, we will not know when we will need to fire and enter that battle ourselves."

"Yes ma'am," Juno said, as he swiftly made sure the order was carried out.

'_Come on Oberath, don't disappoint me now,' _Elizabeth thought. Seeing the flagship appear from a hyperspace jump and position itself behind the other ships, Elizabeth mouth turned into a sneer at it. _'That' s right Oberath, use everyone else to cover you so you don't risk your own neck. You know you're outnumbered here, and you want to make a fast get away.' _It was true, the ratio of replicator to wraith vessels was about 7:1. Many of the replicator ships were out destroying other wraith ships, including supposedly, her own and weren't able to join the fight. Nonetheless Oberath, with the new code included in him as well, couldn't resist an opportunity to take out a whole bunch of wraith at once.

"We await your orders, ma'am," Juno said joining her next to her chair.

"Good, right now stay cloaked. If anyone tries to leave, give chase and fire at will."

In front of the ship, the first rounds of the battle were being exchanged, with a flurry of retaliation from the opposing side.

"One wraith vessel destroyed," Navi reported. "Asurans are taking heavy casualties."

Elizabeth could tell her crew was itching to join the fight, "Hold position."

More ships on both sides exploded in a furious succession, and it was appearing that the wraith were getting the upper hand. Juno looked at Navi's screen with interest, "The flagship's shields seem to be failing ma'am."

"Let's see how much longer he'll make it without running," Elizabeth said bitterly.

"The Asuran numbers are dropping rapidly, as are the wraith. The Asurans taking out ships as their ships are destroyed," Juno reported. "The flagship is moving away from the battle."

"After them!" Elizabeth ordered. "Raise the shields and fire at will!" Juno returned to her side, "Well that didn't take any time at all."

"Indeed," Juno smiled. Elizabeth inwardly smiled at herself for sharing her human emotions with her crew.

"We're taking fire," Navi reported. "Opening fire on the flagship." Her eyes widened slightly. "They're going to open a hyperspace window."

"What?!" Juno shouted for Elizabeth. "They are going to tear their ship apart, it's too damaged!"

"They won't make it," Elizabeth said. "Engine's full power!" Sparks flew from the counsels as the ship was fired at from the other vessels.

"Our shield are failing, power less than 50," Navi reported. "They won't take much more!"

"Divert power from unneeded systems!" Juno ordered.

Suddenly fire shot from the flagship's damaged engines, towards Elizabeth's vessel.

"We're too close," Elizabeth gasped. "Get us away!"

"It's too late!" Juno shouted.

The fire shot though the all ready depleted shield and hit the lower hull. "The hull has been breached," Navi reported. "Fire damage is spreading rapidly."

The flagship opened the hyperspace window and disappeared from sight. "We need to land now to repair our ship," Elizabeth said, recognizing the lost cause. "Is there a planet near?"

"Yes, right next to us," Juno replied. "We maybe able to make it."

"Do it," Elizabeth said. _'Damn you Oberath, you may have squeaked away this time, but next time your day will come.' _

Juno moved back over to stand next to Elizabeth's chair. "Hang on Commander, things are about to get very bumpy." He smiled grimly.

As the ship entered the atmosphere it was tossed around like a kid tossing a ball. Too many times Elizabeth felt herself almost being thrown from her seat. "We're going in too fast," Elizabeth was trying to stay calm.

"The internal dampeners and landing ablities were damaged in the fight." Juno said. "We'll fix them when we land, so either way, this maybe a very rough landing."

Elizabeth peered out the window as trees came closer and closer to the ship. "Still too fast, and the ground level is closing in rapidly." Navi said, trying to keep the panic from here voice.

Suddenly the ship lurched, and the crew was thrown along with their ship into the ground on the planet.


	8. Rebuilding

Chapter 8 - Rebuilding

Sorry about the delay in updating, hopefully updates will be more frequent from now on.

_Atlantis- Control Room_

The senior staff of Atlantis watched in shock and awe as the remaining ships on both sides took each other out. "Where'd they all go?" Rodney asked, blinking at the screen.

Ronon, Sam, and John rolled their eyes. "They blew themselves to kingdom come, McKay." John said. "But the better question is where is the ship that started all this?"

"Probably got destroyed too," Ronon shrugged.

"No, I do not think so," Teyla replied.

"Why is that?" Sam asked.

"I believe I saw the rouge ship, follow another out to here," she pointed on screen. "Next to this planet, after that they both disappeared, but I believe I saw one ship go towards the planet, and then it disappeared."

"Do we have an address?" John asked Chuck who was watching the scene unfold from his station.

"Yes, sir."

"Well what are we waiting for?" Rodney exclaimed. "That ship is probably damaged, and it will take time to repair. We may as well see if they are on the same side, maybe we can work together to destroy the wraith and replicators."

"No," Sam said strongly. "At least not until Morning, when we can see if there are no more ships in the area. I'm not sending you into a possible war zone if it can be avoided." Rodney looked like he was about to protest. "Wait, Rodney. If their ship is damaged it will take a while to fix. So chances are they will be there in the morning. Now get some sleep, I have a feeling you'll need it."

Taking her words as an order, the group disbanded, trying to get some sleep not knowing what awaited them when they gated to the planet. Rodney rushed ahead of them, mumbling something about needing to get some work done.

"Is he all right?" Teyla asked Ronan and John, watching Rodney fly away from them.

Ronan simply shrugged, and John sighed. "I'll go talk to him. You two go get some sleep."

"Good night John," Teyla said.

"Night Sheppard," Ronan added. "And good luck."

_Rodney's lab_

John stood at the door, watching Rodney speed around his lab muttering to himself. He haphazardly tossed some expensive looking equipment in a container, while checking the readings of his new program to track ships. After about the fifth or sixth piece had been thrown in, John decided enough was enough.

"RODNEY!" he yelled, hoping that would stop the scientists frenzy.

Rodney stopped dead in his tracks, and dropped what he was holding.

"That's better." John said normally. "Can I talk to you for a few minutes?"

"What do you want?" Rodney demanded, picking up the dropped instrument.

"You seemed like something was bothering you in the control room. And I have a feeling Carter telling us to wait is only half the problem. What's going on Rodney, you've been obsessing over this ship since we discovered that wreckage?" John sat on a clear space on a lab table.

"Nothing's wrong, I just feel like we're throwing away a very good opportunity." Rodney placed the instrument in its case.

"Such as? The ship will more than likely still be there in the morning Rodney. It had to take a lot of damage in that battle."

"Such as finding potential allies against the wraith and replicator! Such as finding…" Rodney's shoulders slumped as he trailed off.

"Such as finding Elizabeth?" John finished, hopping down to stand next to Rodney.

"No! I mean…"

"You still think she's out there?"

"No! Her duplicate told us she died. Sure she could have been wrong, but still, there's not proof against it," Rodney rambled.

John looked concerned, but stayed silent; lost for words.

Rodney changed tactics, "I mean we're tossing away a perfect opportunity to see how Replicator technology works! That alone could give us a good edge in this. Why aren't _you_ upset over being told that we should wait to go on his mission?"

John shrugged. "I see where Carter is coming from. Its not worth risking our lives over, we could be walking into hostile territory for all we knew after that battle. It wouldn't serve any purpose rushing in and getting ourselves killed." John paused, thinking over his words carefully. "And I know for a fact Elizabeth herself would kill us, if we even tried. If we did go now and died, she would have died in vain; she stayed behind so we could escape those bastards."

"Don't you think I know that?!" Rodney demanded, then fell silent for a few moments. "I guess I just haven't come to terms with it. I mean first Carson and now Elizabeth…"

"I know," John said softly. "We all know how you feel, but it does no good trying to deal with it by not dealing with it."

"Well it seems easier that way doesn't it?" Rodney said. "I mean the universe doesn't stop just because two good people die?"

"True," John agreed reluctantly. "But now its our turn to finish what work they started."

Rodney picked up another instrument and placed it in the much more gently in the case, seeing that he didn't want to talk anymore John walked toward the door.

"Hey Sheppard," Rodney said as he reached the door.

"Yeah," John turned around.

"Thanks."

"No problem. What are friends for? Get some sleep McKay, I have a feeling we have a long day ahead of us."

_Planet where Elizabeth's ship crashed_

Elizabeth looked around the bridge dazed from the force of the crash. "Is everyone all right?"

Juno stood unsteadily, "Yes ma'am. Though the ship was heavily damaged."

"Can we repair it?"

Nami, another technician spoke up, "Yes but it would take several days."

"It was that bad?" Elizabeth asked in disbelief. She had seen the Replicators repair the whole Atlantis Control tower in a matter of hours.

"Yes, not only was the ship's physical structure damaged, but as well as several key components to many crucial systems both in software and physicial form. We have additional copies of the programs, but it will take much time to repair these delicate parts and bring them back to full functionality. It is easier for us to build then repair in this case." Juno explained.

"What are our other options?" Elizabeth asked, eager to get back out and search for Oberath.

"Build a new ship," Nami said. "It would take much less time then trying to repair this one. A few hours at the most. If Lord Oberath found out it was us that shot at him this ship is easy to track anyway. Each ship is equipped with a unique tracker, the new ship would lack one, they are on the home world, but if we keep the same communications signal and disable the tracker on this ship, Lord Oberath will not know the difference."

Elizabeth nodded, "Give the order." Juno nodded at Nami and she rushed off. "Juno, give the order to have the crew ready to move to the new ship as soon as it is complete."

"Yes ma'am."

"I will be in my quarters as well going through our logs getting ready for the move."


	9. The mission

Chapter 9- The mission

_Control Room- early morning_

John awaited his team at the foot of the stairs leading up to the control area. Once they arrived it would be up to the Jumper Bay to grab Jumper One and then on their way to the planet.

Sam looked down from her office to where John stood waiting. _'He looks like this is just a normal mission, not one to go and greet people who are basically the enemy and killed a member of this team he was close to.' _She admired his control, knowing how she felt if it had been a particular member of SG-1 that had died. _'I wonder how in the world he's doing it? He has to have some hope that the duplicate was wrong and she's still out there somewhere.' _She stood there for a few more minutes, then started toward the control area. _'Well I better go and send them off.'_

As Sam reached the overlook in the control area Rodney joined John where he was waiting. Watching the two men she saw Rodney speak while John listened intently. Due to the early hour and lack of people up and about their voices carried up to where Sam stood.

"Teyla and Ronan are running late, I saw them on the way here. They said they'd meet us up at the Jumper." With that the two men set off side by side to the Jumper Bay. Personally Sam was glad to see Rodney's mood had improved since the meeting last night. Leaning against the railing, Sam settled in to wait for the team to set off.

_Jumper Bay_

"Which one are we taking?" Rodney asked, as his equipment began to arrive.

"Jumper One," John replied, walking toward the mentioned Jumper as Rodney's technicians began to load the equipment in the Jumper.

Ronan and Teyla arrived just in time to see Rodney and John enter the Jumper, Rodney yelling at the technicians to be careful with the equipment. "Glad to see that they're finally back to normal," Ronan muttered.

Teyla smiled, "True, but all they really needed was to realize that they are not truly alone."

Hurrying along they entered the Jumper in time to see John and Rodney take their respective seats.

"Finally!" Rodney exclaimed.

"All right," John said, Teyla and Ronan took their seats. " Let's get this show on the road."

Slowly John lowered the Jumper into the Gateroom and Rodney dialed from the Jumpers DHD. _"Good Luck Colonel, and be careful, come back at the first sign of trouble." _Sam said over the radio.

"Thanks and we will," John replied as the Gate sprang to life cutting the radio signal, John moved the Jumper into the open wormhole.

_Planet where the Replicator Ship crashed_

Once through John guided the Jumper through the air, and activated the Cloak. "Okay McKay where is our ship?"

"Hang on," Rodney connected his laptop into the Jumper's systems. "Okay, calibrating my program to work with the Jumper's sensors we should be able to locate the ship." A image of the planet's surface appeared on screen with a blip a ways off from the Jumper's current location.

"I take it that the dot is our ship?" Ronan said, leaning forward in his seat.

"Yes it is," Rodney said, staring at the image. "It and us are the only things on this planet, so thank you captain obvious."

"Well we could have picked something else up," Ronan snapped.

"No," Rodney turned in his seat. "Listen Chewy, this program was designed by me, and it was designed to locate replicator ships using other sensors along with that piece of technology our doubles gave us. There are no flaws, since it was designed by yours truly, who is the resident genius."

"All right McKay," John said, before Ronan tried to shoot. "We'll head towards the dot."

John reactivated the cloak as they left the Jumper. "Okay everyone remember where we parked."

The other members of his team fell in behind him as he led the way to the ship, Rodney was right behind him, lugging his equipment along while Teyla and Ronan brought up the rear.

"What do you think we'll find?" Ronan asked Teyla, mainly to stop himself from hurting Rodney who was complaining about the walk.

"I am not sure," Teyla said, looking around them warily. "We could find anything here."

"What do you think that they are hoping to find?" Ronan asked, meaning John and Rodney.

Teyla smiled sadly, "The same thing we are, whether or not these replicator are a threat."

"Well that and what happened to Weir while she was in their hands," Ronan added.

"Yes, that too, that too," She put a protective hand over her rounding stomach.

John stopped suddenly right before the ship, pulling out a life signs detector to see if there were any replicator about. "Looks like no one is home."

"Really?" Rodney asked. "Wonder why?"

"Not sure, but maybe looking around may give us some answers," John said. "Why don't we split up? Teyla, Ronan, you guys check out living quarters and other areas that weren't damaged in the crash. I'll escort McKay to the bridge so he can get set up there, and then I'll join you. Stay in constant radio contact, and if you find anything before I reach you radio in."

"Right," Teyla agreed.

John took a deep breath, "Let's go."

_Near the Bridge_

John led the way down the corridor with Rodney lagging behind, hauling all his equipment. "How much further is it?" Rodney gasped, staining from the weight.

"Not too far," John glanced at the life signs detector. "Just up this corridor."

"Why don't you carry some of this?"

"Because someone has to keep a look out, and go first," John smirked. "Besides its your fault that you brought so much equipment. What do you need that much for anyway?"

"Because I didn't know what exactly I'd need."

"Right," John turned the corner. "Now quit whining, we're almost there."

They reached the entrance to the Bridge, John placed the life signs detector back in his pocket and held up his gun. Cautiously he stepped just inside the door, panning back and forth he checked to see if there was anything inside. Declaring it all clear, John stepped further and Rodney rushed inside, eyes lighting up. Nearly throwing the cases he was carrying down on the floor he rushed toward the various counsels.

"Can you turn it on?" John asked, taking a casual look around.

"Probably," Rodney was examining a counsel carefully. "But it will take time."

John sighed. "All right, I'll make sure you're started and then go join Teyla and Ronan."

Rodney just nodded absently, pulling out equipment connect to the counsels.

_Living Quarters_

Teyla and Ronan had made their way up from the impassable lower decks to what appeared to be the Living Quarters.

'_Teyla, Ronan what's your status?' _John asked over the radio.

"We are located in what appears to be their living quarters. The lower decks are blocked, and heavily damaged from the crash, we could not make our way through," Teyla replied.

Rodney who had been listening cursed, _"Great that means the engines were damaged as well and are probably not accessible to be repaired."_

"_What were you hoping to fly this ship home?" _John asked.

"_Do you know how valuable this technology is? I need more time to study it, and my teams, and equipment" _Rodney demanded, fiddling with the counsel. _"It's not like we can exactly tow it home with the Jumper."_

Teyla and Ronan slowly entered the next living quarters they came across while the two bickered back and forth.

"_Anyway," _John said finally. _"Have you find anything of interest?"_

"Not yet," Teyla began before Rodney interrupted.

"Finally!" Rodney cried out, as the counsels in the Bridge sprang to life. "Now we can get somewhere!"

"_Rodney just got the counsels working, so I'll come find you and help you search. Sheppard out." _

After John had signed off, Teyla and Ronan further examined the quarters they were in. These quarters were much larger then the ones they had visited previously. Something Ronan noted aloud to Teyla.

"It could be the quarters of the captain of this ship," Teyla replied, looking what appeared to be a closet.

"Maybe," Ronan agreed, stepping into the next room. "Teyla."

"What is it?" Teyla joined him. This room was the bedroom, but the bed had been hastily thrown back into some sense of order, and the ornaments that must have hung on the walls were missing.

"Looks like they left in a hurry," Ronan noted, taking a closer look at the bed.

"Yes, so it would seem. But what would cause them to leave so quickly. They are the only ship here since the battle yesterday," Teyla opened another closet in the bedroom. Looking around the closet while Ronan moved around the room; looking on the floor Teyla saw something of interest. Reaching down she turned a small piece of cloth over in her fingers revealing a red, white and blue pattern the two aliens had seen on their friends clothing. "Ronan," she called, voice shaky.

"Yeah?" Ronan joined her as she stood. "Is that?"

"Yes, a patch from an Atlantis uniform," Teyla's hand trembled as she held it.

"It's clean," Ronan took it and examined it. "No damage, but what is it doing here?"

"I do not know, but clearly events are not as they have been told to us. How else would the patch be here? None of us have come across the replicator since Elizabeth sacrificed herself, and then our duplicates. It only makes sense that this patch is hers."

Ronan nodded, "Let's go find Sheppard, he and McKay will want to see this. That and maybe McKay will be able to find out whose it is."

Hurrying Ronan and Teyla rushed out of the quarters to find the others.


	10. United We Stand, Uphill Battles

Chapter 10- United We Stand- Uphill Battles

Sam rushed out of her office at the sound of the Gate activating. "Any IDC?" she asked Chuck.

"Colonel Sheppard's ma'am," He replied.

"Let them through, I'll meet them in the Jumper Bay." Sam rushed up the stairs to the Jumper Bay. _"They're back early," _she thought as she climbed. _'Too early, if the replicators had all ready gone, Rodney will should be driving John nuts checking out the replicator technology. And if they hadn't gone the team would probably be trying to make an alliance.'_

Waiting, rather impatiently Sam watched as the Jumper rose from the Gateroom below. Rather slowly she watched as John moved the Jumper into place and the team with forlorn faces exited.

"What happened?" Sam asked, as they neared. "I didn't expect you so soon."

Watching their faces, and trying to see what was the matter, Sam notice Teyla seemed to be cradling something in her hand. "What happened on the planet?"

Finally it was Rodney who spoke, "We found the ship, and it is a rouge ship." He paused, his voice nowhere near the usual chatter it usually held. "It's mission is to whip out the Replicators and the Wraith, using the Replicators' own technology against them."

"Did you encounter the crew?" Sam asked, still puzzled at what was the matter.

"No," Ronan spoke up. "They must have built a new ship, eager to get back into the fight, or at least the log hinted to it. The one we found must have been deemed unfit for battle it was completely abandoned."

"Did you find anything of interest?" Sam asked, her eyes once again drawn to what Teyla was holding.

"Yes, this," Teyla replied very softly. She opened her hands to reveal the Atlantis uniform flag patch.

Sam's eyes widened at the sight of it, "Is that?" She had to fight to keep her voice from breaking.

"Yeah it is," John said, his eyes constantly on the patch. "Rodney checked the logs of the ship, their mission is led by Elizabeth, captain of the ship."

'_This is going to through the IOA for a loop,'_ Sam thought, hoping someone could see their side, and that telling Jack straight off would increase those odds. "Go to the infirmary, and get something to eat, I need to contact Earth about this." She cut John off before he could say anything. "I know you want to see if you can find her, but right now she's seen as a security risk, though I doubt she is, and that's all the IOA will see right away. And like it or not we need the IOA support if we don't want any trouble for her. I'm all for bringing her back, you must understand that, and if I have anything to do with it we will."

"Fine," John conceded. "Come on, the Doc will want to see us."

Sam watched John lead his team away. Going down the stairs after them she went to Chuck. "Dial Earth," She ordered, looking grim, preparing herself for a battle.

_Mess Hall_

As soon as they were cleared from the infirmary the team decided to wait it out together, and take Sam's advice. Sitting and eating in silence while the other tables conversed about the happenings in Atlantis and various projects they were working on. Kavanaugh could be heard complaining loudly about Rodney's correction of his calculations from the day before, that he was certain they were still correct; which didn't even trigger a response from the usually argumentative scientist. Teyla sat in a daze fiddling with the food on her plate, while Ronan stared off into space next to her. The unusual silence brought some uneasy glances from the tables who were closest.

Radek entered the Mess Hall to see the unusual scene, seeing the other tables full he decides he has no other choice but to sit with the silent team. Taking a deep breath Radek braced himself and approached the table.

"umm…Colonel can I sit here?" Radek asked softly. "Everywhere else seems to be full."

"Sure," John replied somewhat distantly.

Radek took a seat next to Rodney and began to eat, feeling somewhat out of place. "I just came from the Control Room, and saw something interesting." He was trying to start any form of conversation to ease the mood of the table.

"What's that?" Rodney asked, the table's mood suddenly spiking suddenly.

"Well I had a meeting with Colonel Carter this morning about the Jumper Research we've been doing, and when I went to meet her she was in the middle of a video conference with General O'Neill about Elizabeth," He paused seeing he had everyone's undivided interest now, including several tables around them he continued. "Something about you had a mission to find a rouge replicator ship and through the logs found Elizabeth is alive leading a resistance against the wraith and replicators."

"What did he have to say?" Ronan asked.

"Something about the IOA is going to have a field day, and he would have endless meetings, but he is going to fight to bring Elizabeth back to Atlantis."

That perked everyone's moods up. "Did he give a hint if the IOA would even go for the idea?" Rodney asked.

"No idea, I left as soon as I saw I wasn't going to be able to meet with the Colonel I left," Radek took a drink. By this time the entire mess hall was silent, hanging on their words. "Is she really alive?"

"Yes," Teyla spoke up. "Besides the logs we found the patch of an Atlantis uniform. It could only have come from Elizabeth's."

Radek muttered something in Czech, Ronan looked up. "Here comes Carter."

Their heads turned as the new leader joined them. "Can I sit here?" she asked.

"Sure," Rodney said, eager to hear news as she fell into the only unoccupied seat. "How are things with Earth?"

Carter sighed, "I'm not sure yet, we have Jack on our side, but I'm afraid that it won't be enough. The IOA will only see a security threat, they have no idea what Elizabeth has done for this base, and how much it needs her."

The entire rooms faces fell, and Sam's heart went out to them. "There has to be a way to show those bureaucratic idiots what Elizabeth has given to the success of this expedition," Rodney said, slamming his fist on the table.

"You mean besides sacrificing herself in order to let us escape?" Ronan asked.

"Well yeah," Rodney said. "Let's start with that."

"Maybe we can all make a personal message to send to the SGC and show our support?" A scientist sitting at the other tables suggested, the others looked at each other and murmured their support for the idea.

Sam looked thoughtful for a moment, "You know that may just work." She grinned. "Just have it ready by our next scheduled check-in with Earth in a week. I'll let General Landry and Jack know to expect it."

Eager to begin the members of the Atlantis expedition began to bounce around ideas about what should be included in the messages and how it should be formatted. Sam smiled at the effort that was being put into this, and hoped that in the end it would help sway the IOA to some degree.

_Elizabeth's ship_

Elizabeth, wearing the clothes from the battle, strode into a partially lit room with a stressed expression on her face. In the centre of the room there was a holographic communication device, with seats surround it. She paused slightly as she neared the device, noticing that one of the seats had been moved. Her green eyes scanned the room to see a shadowy figure sitting in the corner of the room. Sighing, she positioned herself so that the hologram would have to face away from the figure when it activated.

"Elizabeth," Oberath greeted, appearing from the device.

"Lord Oberath," Elizabeth bowed in greeting, somehow keeping the disgust from her face. "To what do I owe this honor?"

"How fares your battle with the wraith?"

"Very well," Elizabeth took a seat. "We managed to defeat them, though our ship suffered heavy damage in the battle. I apologize that we could not come to your aide when you faced the wraith yourself, that was when their onslaught on us was at the worst. Our ship suffered heavy damage that has just been fixed."

"All is well now I trust," though Elizabeth did not reply Oberath continued. Though it is quite all right, we managed, but it would have been a great asset to have you in the battle alongside us."

"Thank you Lord Oberath."

"Are you pursuing any more wraith in your area?"

"Not at the current time, we have been monitoring their movements and it seems they have been moving out of our sector, we are in the process of plotting a course to pursue them."

"I see, well I have another task I can only trust you to take care of."

"What is that my Lord?"

"There is a planet that our intelligence reports that the Wraith have taken an interest in due to the abundant human life there. I have some new captains I would like to train using the wraith in that sector, but I cannot do it because as we both know Wraith are much more difficult to kill when they have recently fed. It is my hope that they will land there, hoping to feed and then the captains can destroy them due to intelligence we have planted within their ranks. Your ship is the closest."

"Of course Lord Oberath."

"Very well, I am sending the coordinates now. Good Luck."

"Yes Lord Oberath."

"And commander, I do want proof that they all are indeed destroyed if you can."

With that Oberath's hologram disappeared from sight. Cursing Elizabeth rounded the holographic device. "Can you believe this?" she demanded of the figure in the corner.

"Well it is Oberath lass," a familiar Scottish lilt came from the figure who stood. "What else do you expect from him? You're not really going to do it are you?"

Elizabeth sighed. "Of course not Carson. It's a test, I have a feeling that he knew that battle was set up, and that it was us shooting at him."

"Then what are you going to do?" Carson stepped into the light, watching the former leader of Atlantis with interest. He had followed her faithfully when they were in Atlantis and he wasn't about to stop now, things may have changed with them both; he being Michael's captive the past year or so and her part Replicator, but she was still the same leader that had ruled the city they had once called home. He would have done anything for her then, and still would today. "He asked for proof."

"I'm not sure." Elizabeth sat down in another seat, and Carson sat across from her.

"You could always contact Atlantis," he suggested gently, though visibly readying for a battle.

"NO!" Elizabeth's eyes widened at the suggestion. "We can't contact Atlantis, Carson, how often do we have to go through this? You know I would love to let everyone there know the truth, but all Earth will see me as now is a security threat, I'll be shot on sight. And you've been dead for a year, not to mention living among a bunch of Replicators. The IOA will see you as compromised, so you'll be at risk too. Our contacting them will only reopen old wounds that I'm sure have just begun to fade." Her face fell at the thought.

"You said your patch from your uniform was gone right? Well maybe the team found it, we should have come in on their long range sensors."

"No we were too far out in the galaxy, I wish that were the case though. It would be nice to see them again even for a little bit."

'_Especially a certain someone.'_ Carson thought but he kept to himself. "I'm not sure what you are going to do then lass."

"I'm not sure either, let me think on it a bit, alone." Carson hesitated to get up to leave. "Please, I'll let you know as soon as I come to a decision."

"Very well lass, I'll leave you alone to think. I'll probably be in the infirmary , so you can find me there, maybe we can make a breakthrough."

Elizabeth chuckled as he left and shut the door. "You say that everyday Carson, but its nice to keep that hope alive."

_A/N: Come on, you didn't think I'd fix on mistake and keep one still messed up did you? Chapter 11 coming soon. _


	11. Mission of the Lost Doctor

**Chapter 11- Mission of the Lost Doctor**

** A/N-** Sorry for the delay in update for so long, real life, and the long vacation of my muse caught up to me. Hopefully the updates won't be so far apart from now on. Thanks as always for the feedback, it helps to keep me going. And without further ado (after all you have waited long enough :D)-

* * *

Carson left Elizabeth, but did not go to his infirmary right away, wishing to unwind before he settled back into work. As he wandered the corridors passing replicators greeted him cheerfully as they went about their business. Carson still felt overwhelmed when it came to these replicators, their friendliness wasn't at all what he was accustomed to when it came to their kind. Still he returned the gesture to his new comrades, though at times all he wanted to do was run and bury himself into the work that awaited him in his infirmary.

_ His infirmary, which was aboard a replicator ship. _That was a thought he was still getting used to. Elizabeth had noticed his withdrawn behavior still remained even about a month after he was rescued from Michael, despite the attempts of everyone to welcome him aboard and make him feel a part of the crew, and had crafted the space that he felt most comfortable in. To his surprise, after discovering what exactly it was that he did for a living a few replicators had come forward to learn, interested in helping humans fight illness and making the galaxy a better place in that way. For beings that had no need for the knowledge they were very eager to learn, and Carson appreciated the help since they had a few close calls with malfunctioning nanites. Back in his element, saving and helping better lives, Carson thrived once more Elizabeth had happily noted watching. Rounding the corner to the corridor that led to the infirmary Carson thought back to how he and his assistants had begun their current mission.

* * *

_ It had started with test over the new treatment they had been learning._

_ "I wish to help people all over the galaxy once our purpose is done on the ship," Jai, one of his assistants said suddenly._

_ It made Carson pause, "I see no problem with that, there can never be enough doctors." He wondered if they all had the same desire. What will you do once this thing is over Sera, Lukas?"_

_ "I wish to do the same thing," Sera said sadly while Lukas nodded in agreement. "But we can do nothing with this great knowledge."_

_ "Why do you say that lass?" Carson asked, surprised at how sad she sounded._

_ "We are replicators," Lukas said matter of factly. "No one will accept us into their people, because of what we are."_

* * *

That conversation got Carson thinking, these people would have no place to go or nothing to do once the war was done. They were to some degree programed to do what jobs they preformed, yes it was true that interaction with Elizabeth's nanites had given them some of the human traits such as free will, but the programing of the nanites still dictated what was done daily with no flexibility. Looking at their faces he had seen the honest desire to be more then what they were then; which with this crew, meant others shared the same hope. In Carson's eyes every person deserved the opportunity do what they wished to do without barriers and he set about hoping to solve the issue; something his assistants had dove into headfirst. He knew it wouldn't be a simple case of medical science so he asked Elizabeth if he could enlist some scientists to help. Once a solution was found it would be offered to all those who wished to take it.

"Dr. Beckett!" Jai and Sera called excited once he entered the room.

"What is it lasses?" He asked, shrugging on his lab coat.

"I think we have something." Jai said.

"Really?" Carson was relieved, he didn't know how much longer their spirits could take the constant disappointment.

"Yes," Sera said. "Our scientists believe they can re-write the code of our nanites to accept the integration with human tissue, making them organic."

"The only problem is that our new tissue, would decay after time due to the lack of proper DNA, and therefore lack of proper cell structure," Jai added.

Carson looked thoughtful. "The Asgard had a similar problem with their cloning, the DNA became so broke down their cloned bodies were starting to fall apart. DNA tells the cells what to do, how to survive."

"We do not have enough, or will have enough to have it work with the human tissue samples we have," Sera pointed out, looking slightly crestfallen.

"We'll have to see if we can get it to work somehow," Carson said optimistically. "We can get together with the scientists later to see if they have any ideas too."

"Right," agreed Jai. "Let us get to work then."

Carson, Jai and Sera were joined by Lukas soon after. For hours the four tirelessly worked to hope to find a solution. It was in that state that Nami found them.

"Dr. Beckett?" She asked pausing just inside the doorway.

"Yes," Carson looked up from his microscope.

"The commander wishes to speak to you, she is in her quarters."

"Thank you Nami." Carson laid his coat on his chair. "I'll be back in a bit. Why don't you take a break while I'm gone? This stuff won't go anywhere."

"Sure Dr. Beckett," Lukas said.

Carson left at that eager to hear what Elizabeth had decided.

* * *

**A/N- **Sorry this chapter is so short, the next one will be longer.


End file.
